At the last SynBERC retreat SynBERCers decided that solving the challenge of automated DNA assembly/cloning would be a priority for the center. COG will be tasked with drafting a report for the upcoming NSF visit in March(?) that evaluates current assembly approaches and proposes a path forward. This page is just getting started, please add/edit!
- Maintain communication across labs on status of automated assembly projects.
- Produce a report with evaluation of current assembly approaches and recommendations for going forward.
What are the goals for COG?
Proposed based on SynBERC meeting / conversations since:
- Stay up to date with current automated cloning research projects taking place in SynBERC labs
- Get the ball rolling for solving the automated cloning problem in the short term
- 1/2 the meeting?
- Brief updates from each of the groups? one longer presentation each month about one project?
- Something else?
Getting the ball rolling for solving automated cloning
- Define the problem we want solved
- Specify the possible solutions
- Evaluate / Act on solutions
- Combinatorial libraries of assembled parts (Wendall, UCSF iGEM team project)
- Automation of standard BioBrick Assembly (Registry)
- Automation of assembly independent of BBs (Synth companies?)
Specify Possible Solutions
- Decentralized approach
- We make cloning easier by using some automation combined with "normal" individual cloning approaches. For example, each lab buys a Qiacube to partially automate minipreps and restriction digests. Then ligations and transformations are done by hand at the bench.
- Centralized academic facility
- We find the resources to start an assembly facility similar to how sequencing facilities are set up on campus
- Outsource to DNA synthesis company
- We work with a DNA synthesis company so that they can offer commercial automated cloning services. How do we ensure that such a partnership wouldn't fall apart as soon as a big synthesis order comes along? Automated cloning may be too small a market and/or too large a problem for DNA synthesis companies to tackle right now?
Evaluate / Act on Solutions
- Registry hires more staff to do process engineering
- Trial QIAcube / other "cheap" robots for distributed approach
- Figure out how big an assembly order iGEM + labs using parts could put together for a Synth company (George suggestion)
- Go talk to Synth companies see if they'll do this.
- Plot the cost of synth vs. assembly over time for particular length scales (drew's suggestion)
- Any weekday's particularly bad for certain groups? (Weds at MIT)
- Join the mailing list
- Chris Anderson
- Adam P. Arkin
- Austin Che
- George Church
- Jeffrey Dietrich
- John Dueber
- Will Holtz
- Jason R. Kelly
- Tom Knight
- Sergio Peisajovich
- Randy Rettberg
- Reshma Shetty
- Lane Weaver
- Reid Williams
- Josh Kittleson
- Harris Wang
- Caroline Ajo-Franklin
- Meagan Lizarazo
- Julie Norville
- Leonard Katz
- Swapnil Chhabra